title: The miR-194-5p/BCLAF1 module is responsible for maturation block, cell fate and treatment susceptibility in AML.

status: Public on Dec 20 2017

first: Joost

last: Martens

department: RIMLS

institute: Radboud University

summary: miRNAs deregulation contributes to cancer. miR-194-5p is up-regulated by the HDAC inhibitor (HDACi) SAHA, negatively modulating BCL2-associated transcription factor 1 (BCLAF1). We prove that the miR-194-5p/BCLAF1 equilibrium regulates differentiation, survival and self-renewal of normal progenitors and acute myeloid leukemia (AML) blasts. This equilibrium is perturbed in AMLs resulting in highly expressed BCLAF1, suppression of miR194-5p, consequently, locking cells into an immature, potentially ‘immortal’ state. HDACis reverse this scenario relocating BCLAF1 from the nucleus to a peri-membrane ring-like cytoplasmic structure, sensitizing the cells to differentiation or apoptosis. miR-194-5p and BCLAF1 are significantly deregulated in a cohort of 60 primary AMLs and get restored by HDACi. Our findings connect responsiveness to treatment to re-instatement of miR-194-5p/BCLAF1 balance. These findings might be exploited for (epi-based) anti-leukemia therapy.

overall_design: U937 cells were transduced with constructs expressing mir-194-5p or a scrambled (sc) control. The transduced cell lines were used for DNAseI-seq analysis following previously published protocols (Neph et al., 2012)

first: Carmela

last: Dell’Aversana

first: Cristina

last: Giorgio

first: Loredana

last: D’Amato

first: Gabriella

last: Lania

first: Filomena

last: Matarese

first: Sadia

last: Saeed

first: Valeria

last: Petrizzi

first: Concetta

last: Ingenito

first: Hendrik

last: Stunnenberg

middle: H

first: Lucia

last: Altucci


title: Investigation of thyroid hormone induced gene expression in liver tissue of different thyroid hormone receptor mutants

status: Public on Feb 01 2018

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary: We used microarrays to investigate differential gene expression in different thyroid hormone receptor beta mouse models. Hypothyroid wild type, TRbeta KO and TRbeta GS mutant mice were treated with T3 or vehicle alone. Microarray analysis revealed that the gene expression pattern in TRbeta GS mutant mice was similar to that in TRbeta KO mice.

first: L

middle: C

last: Moeller


title: Lipid addiction via Fatty Acid Synthase activates PI3K signaling in B cell non-Hodgkin’s Lymphoma (bNHL) [Illumina]

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

country: USA

institute: NASA Ames Research Center

summary: Dysregulated lipid metabolism is an oncogenic mechanism that leads to increased de novo fatty acid biosynthesis via elevated expression of fatty acid synthase (FASN) in cancer. FASN catalyzes biosynthesis of (C16) palmitic acid by using Acetyl CoA, malonyl CoA and NADPH as substrates. Palmitic acid and its derivatives participate as signaling lipids andinvolved in the regulation of receptor functions associated with many biological processes. and furtherThis includes contribute formation of cell structures, and all these processes which are essential for both normal and malignant cell growth and proliferation. In this study, we investigated the biological impact of FASN inhibition in B cell Non Hodgkin Lymphoma (bNHL) cells using FASN inhibitors Cerulenin and other novel agents (TVB3166, TVB3567).  Inhibition of FASN resulted in a dose dependent increase in cell death and apoptosis in the bNHL and primary tumor cells. Transcriptomic and comprehensive systems biology analysis of cerulenin, TVB3166 or TVB3567 treated bNHL cells revealed conserved activation of (TNF) immune and PI3K signaling, and inhibition of cell cycle pathways as prominent responses to FASN inhibition. Cell fractionation and western blot analysis of cCerulenin treated cells showed translocation of TNF receptor adaptor proteins (TRAF2 and RIP), docking of AKT and PI3K/p110 subunits to cell membrane and activation of PI3K/AKT pathways by phosphorylation in SUDHL2 and SUDHL4 bNHL cells, while these mechanisms were constitutively active in cerulenin treated SUDHL10 bNHL cells. Disruption of lipid raft formation by methyl β cyclodextrin inhibited PI3K signaling and downregulated FASN expression in SUDHL10 cells.  Subsequently, we observed that combination of FASN (cerulenin) and PI3K (Buparlisib) inhibitors resulted in synergistic cell death in bNHL cell lines and increased apoptosis accompanied with down-regulation of FASN expression in bNHL cell lines and primary cells, implicating the importance of PI3K in the regulation of lipid metabolism. Further mass spectrometric evaluation of cerulenin and Buparlisib treated DLBCL cells fed with C14C glucose, synergistically decreased the biosynthesis of palmitic acid and its derivatives compared to single agent treatments. Our conclusions from these investigations suggest that simultaneous blocking of PI3K and FASN is likely to exert stronger inhibition of lipid metabolism and enhance cell death in lymphoma.

overall_design: For genome-wide expression profiling of SUDHL4 cells treated with 12.5uM Cerulenin, 5.6uM TVB3567, or LDS for 48 hours, Human HT-12 BeadArray chips (Illumina, San Diego, CA) were used. RNA was isolated using RNeasy Minikit (Qiagen), following instructions recommended supplied by the manufacturer. Purity and the yield of isolated RNA was determined using Bioanalyzer. These experiments were performed in biological triplicates. All replicate samples were run individually. Total RNA of 500ng per sample was amplified using AmbionTotalPrep, and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C, the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. Data were corrected through COMBAT correction, quantile normalized, collapsed to genes from probes, then imported into MultiExperiment Viewer, MeV for analysis. Statistically significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction and false discovery rate (FDR) < 0.05 that resulted in a list of significant genes.

first: Ravi

last: Dashnamoorthy

first: Nasséra

last: Abermil

first: Andrew

middle: M

last: Evens


title: Lipid addiction via Fatty Acid Synthase activates PI3K signaling in B cell non-Hodgkin’s Lymphoma (bNHL) [Affymetrix]

overall_design: SUDHL10 and Raji cells were treated with Cerulenin for 48 hours, RNA was isolated using RNeasy Minikit (Qiagen), following instructions recommended supplied by the manufacturer. Purity and the yield of isolated RNA was determined using Bioanalyzer. These experiments were performed in biological triplicates. Microarray experiment was performed on Affy Human Gene Chip 2.0, at UMASS Medical School Genomic Core facility. Data for lines were background adjusted and quantile normalized using RMAExpress. Statistically relevant genes were determined by applying LIMMA with a FDR < 0.05 that resulted in 1092 significant genes for the Raji experimental group and 1600 significant genes for the SUDHL10 experimental group.


title: Interleukins 12 and 15 induce cytotoxicity and early natural killer cell differentiation in type 3 innate lymphoid cells

status: Public on Jan 09 2018

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

type: Expression profiling by high throughput sequencing

summary: Type 3 innate lymphoid cells (ILC3s) fulfill protective functions at mucosal surfaces via cytokine production. While their plasticity to become ILC1s, the innate counterparts of type 1 helper T cells, has been described previously, we report that they can differentiate into cytotoxic lymphocytes with many characteristics of early differentiated natural killer (NK) cells. This transition is promoted by the proinflammatory cytokines IL-12 and IL-15, and correlates with expression of the master transcription factor of cytotoxicity eomesodermin (Eomes). As revealed by transcriptome analysis and flow cytometric profiling, differentiated ILC3s express CD94, NKG2A, NKG2C, CD56 and CD16 among other NK cell receptors, and possess all components of the cytotoxic machinery. These characteristics allow them to recognize and kill leukemic cells. Therefore, ILC3s can be harnessed for cytotoxic responses via differentiation under the influence of proinflammatory cytokines.

overall_design: Expression profiling (RNA-Seq) of NKp44+ innate lymphoid cells (ILC) derived from pediatric tonsils and spleens of NOD SCID-/-γc-/- mice reconstituted with human hematopoietic progenitor cells.  Three experiental groups were compared: not cultured ILCs, ILCs cultured with IL-2 and IL-7, and ILCs cultured with IL-12 and IL-15.

first: Ana

last: Raykova

first: Frank

last: Lehmann

first: Robert

last: Ivanek

first: Daniela

last: Finke

first: Christian

last: Münz


title: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 1]

status: Public on Dec 03 2017

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. Additionally, upon HNRNPU depletion, chromatin interactions between A-type (active) and B-type (inactive) compartments increase significantly but those among same types of compartments decrease significantly, which associate with global gene expression changes. While TADs remain largely invariant, both inter- and intra-TAD interactions increase significantly in A-type compartments but decrease in B-type compartments. Mechanically, HNRNPU complexes with structural proteins CTCF and RAD21; depletion of HNRNPU specifically weakens the bindings of RAD21 to the chromatin, which is highly correlated with the weakness of chromatin loops.

overall_design: ChIP-seq data of CTCF, RAD21 in Ctrl and HNRNPU KD AML12 cells.

first: Hui

last: Fan

first: Pin

last: Lv


title: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [Hi-C]

overall_design: Hi-C data  in Ctrl and HNRNPU KD AML12 cells.


title: Genome-wide maps of nuclear lamina interactions in AML12 cells upon HNRNPU KD [DamID]

overall_design: LAMINB1 DamID data in Ctrl and HNRNPU KD AML12 cells.


title: Abnormal intragenic transcriptional activation in the BRE gene in MLL-rearranged and MOZ-CBP+ AML

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

country: Netherlands

summary: High BRE gene expression in MLL-AF9+ acute myeloid leukemia (AML) is associated with a favorable prognosis, while high MECOM expression confers a very poor prognosis. ChIP-seq and RNA-seq experiments on primary human MLL-AF9+ AML samples showed more pronounced signals in samples with high MECOM expression, explaining its high expression. Between samples from the two MLL-AF9+ AML subgroups, promoter marks were located at the same position at the MECOM locus. In contrast, intragenic active promoter marks in BRE were exclusively present in samples with outlier high BRE expression. 5’ RACE and RNA-seq showed biallelic transcription of a novel BRE transcript starting adjacent to the active promoter marks followed by downstream exons. RT-qPCR detected the novel BRE transcript in >50% of adult and childhood MLL-rearranged (n=56) but also MOZ-CBP+ AML (n=20), while it was virtually absent in other samples (n=145, p<0.0001). The novel BRE transcript and active promoter marks were also absent from large publicly available datasets, underlining the uniqueness of this novel BRE transcript.  Genome-wide analyses of MLL-AF9+ samples showed abnormal intragenic H3K4me3 marks in 90 genes exclusively in high BRE samples. Of these genes, expression of exons downstream versus upstream was most discriminative for BRE. Luciferase reporter assays using the intragenic BRE promoter showed that it was transactivated by MLL-AF9. The new BRE transcript may encode a BRE isoform that lacks part of the N-terminus. Importantly, we detected a new in frame CHORD1-BRE fusion in a case with relapsed AML. The BRE fusion occurred in the same region as intragenic transcription activation in BRE in MLL-AF9+ AML. This work identifies strong abnormal intragenic transcription activation resulting in the formation of a new BRE transcript in MLL-AF9+ and MOZ-CBP+ AML. Future studies should reveal whether alternate BRE contributes to AML pathogenesis.

overall_design: Genome-wide (ChIP-seq) binding of MLL, H3K4me3, H3K27ac, in MLL-AF9 positive AML patients.

first: Koen

last: Prange

first: Anna

middle: E

last: Marneth

first: Matthijs

middle: A

last: Sanders

first: Saskia

last: Bergevoet

first: Nicollo

last: Tesi

first: Askar

last: Obulkasim

first: Eva

last: Janssen-Megens

first: Bowon

last: Kim

first: Nilofar

last: Shariff

first: Marie

middle: L

last: Yaspo

first: Adil

last: Hinai

first: Elodie

last: Stoetman

first: Jeroen

last: Knijnenburg

first: C

last: Zwaan

first: Marry

last: Van den Heuvel-Eibrink

first: Torsten

last: Haferlach

first: Maarten

last: Fornerod

first: Joop

last: Jansen

first: Peter

middle: J

last: Valk

first: Bert

last: Van der Reijden


title: Generation of virtual memory from relatively highly self-reactive is a mechanism of self-tolerance

status: Public on Nov 09 2017

first: DBM Bioinformatics

last: Core Facility

summary: Virtual memory T cell show an intermediate expression profile in between naïve and true memory T cells. Most plausible explanation is that they trigger partial memory differentiation program.

overall_design: Analysis of naïve, virtual memory, and true memory CD8+ T cells

first: O

last: Stepanek

first: R

last: Ivanek

first: D

last: Mueller


title: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq]

first: Bo

last: Wen

overall_design: RNAseq data in Ctrl and HNRNPU KD AML12 cells.

first: Hui

last: Fan

first: Pin

last: Lv


title: The novel BETi BI 894999 represses super-enhancer associated transcription and synergizes with CDK9 inhibition in AML by induction of apoptosis

status: Public on Mar 02 2018

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for acute myeloid leukemia (AML) in preclinical models and are currently being evaluated in clinical trials. This work presents a novel potent and selective BET inhibitor (BI 894999), which has recently entered clinical trials (NCT02516553). In preclinical studies, this compound is highly active in AML cell lines, primary patient samples, and xenografts. HEXIM1 is described as an excellent pharmacodynamic biomarker for target engagement in tumors as well as in blood. Mechanistic studies show that BI 894999 targets super-enhancer-regulated oncogenes and other lineage-specific factors, which are involved in the maintenance of the disease state. BI 894999 is active as monotherapy in AML xenografts, and in addition leads to strongly enhanced antitumor effects in combination with CDK9 inhibitors. This treatment combination results in a marked decrease of global p-Ser2 RNA polymerase II levels and leads to rapid induction of apoptosis in vitro and in vivo. Together, these data provide a strong rationale for the clinical evaluation of BI 894999 in AML.

overall_design: We performed ChIP-seq experiments in 22 samples covering 4 different cell lines and 3 different antibodies (H3K27ac, BRD4, RNA Pol-II). Some experiments were performed using 2 biological replicates. Technical replicates (if available) were merge in the respective FASTQ files. All published ChIP-seq results were derived from merged biological replicates for the specific ChIP-seq experiment with respect to the cell line specific input. Unique numbers in the sample/result names assign the FASTQ files to their processed output files. We also performed Quant-seq in-vivo experiments in 27 cell-line derived xenografts (MV-4-11-B) using 3-4 replicates. Control samples are detonated as the Natrosol treated samples. Lastly, we performed RNA-seq experiments in 38 samples covering 6 different cell lines. These experiments were performed using 2 biological replicates. Note, the compound mentioned in the paper LDC000067 is identical to EX00101218 - these are two different identifiers for the same molecule.

first: Fabio

last: Savarese

first: Norbert

last: Schweifer

first: Onur

last: Kaya

first: Janina

last: Beck


title: Differential gene expression in the liver of zebrafish larvae exposed to 1 mM inorganic arsenic from 4-120 hpf

status: Public on Nov 12 2017

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: The goal of this study is to compare gene expression levels in the livers of larval Tg(fabp10:nls-mcherry) exposed to 1 mM inorganic arsenic from 4-120 hpf to the unexposed siblings. Samples were collected from Tg(fabp10:nls-mcherry) zebrafish larvae that were derived from incrossed parents of the same strain. The background of transgenic lines were typically from mixed outcrosses of the transgenics to AB, TAB5, and TAB14 strains when regenerating the lines as the working stocks aged. All samples were collected at approximately 120 hpf - natural spawning at 8:30-9:00AM EST on day zero, samples were collected at 8-10AM  EST on day 5.

overall_design: Zebrafish larvae that were untreated (control)  or those exposed to 1 mM inorganic arsenic from 4-120 hpf were anesthetized and the liver was microdissected from 10-20  larvae and pooled per treatment group. The transgenic line Tg(fabp10:nls-mcherry) was used to facilitate microdissection of the liver.   RNA was extracted using the Zymo Quick-RNA Micro Kit with on-column DNase treatment. Libraries were prepared according to Illumina Truseq RNA sample prep kit, version 2, followed by Ribo-Zero Gold treatment.

first: Kathryn

last: Bambino

first: Chi

last: Zhang

middle: S

last: Edepli


title: miR-975 overexpression effect on Drosophila cell lines

status: Public on Nov 30 2017

city: Ann Arbor

first: Yang

last: Lyu

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: We overexpressed the conspecific miR-975 in the cell lines derived from multiple Drosophila species (i.e. S2 cells from Drosophila melanogaster; ML82-19a cells from Drosophila simulans and WR-Dv-1 cells from Drosophila virilis). Comparison of the miR-975 effect between different cell lines provide insight into the rewiring of regulatory network through the evolution of new microRNA.

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila virilis

overall_design: We examined conspecific miR-975 effect in three cell types. Empty vector (pUAST-only) was transfected as control. Two biological replicates were done for each treatment.

first: Zhongqi

last: Liufu

first: Juan

last: Xiao

first: Chung-I

last: Wu

first: Tian

last: Tang


title: miR-1199-5p and Zeb1: a novel double-negative feedback coordinating EMT and tumour cell invasion (miRNA-seq)

first: DBM Bioinformatics

last: Core Facility

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed miRNA-sequencing in a detailed time course of a TGFbeta-induced EMT in normal mammary gland cells and discovered 32 strongly, differentially expressed miRNAs.

overall_design: MiRNA profile of time-resolved TGFbeta-induced EMT of NMuMG cells.

first: Maren

last: Diepenbruck

first: Stefanie

last: Tiede

first: Robert

last: Ivanek

first: Fabiana

last: Lüönd

first: Meera

last: Saxena

first: Nathalie

last: Meyer-Schaller

first: Gerhard

last: Christofori


title: Gene-expression profiling in desmoplastic small round cell tumors

status: Public on Aug 15 2017

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: The study provides evidence that DSRCTs are characterised by a high degree of plasticity governed by the MErT/hybrid-partial EMT/EMT process and that, within this three-way switching, the hybrid/partial and MErT classes are also enriched in stemness. The expression of miRNA-21 in all three classes indicates pluripotency as an additional trait of DSRCT cells. These findings are consistent with either the broad histological spectrum of DSRCTs or their poor response to treatments, including tailored treatments against AR-positive DSRCTs. The study also demonstrates that DSRCTs carry a PD-L1 signature corresponding to “immunological ignorance” and highlights the fact that this signature is closely histotype-related and immuno-context-dependent. Finally, the results show that ISLR/Meflin, a further marker of pluripotency, is co-expressed with PDGFRα in DSRCT cells, albeit at a low level and that, in line with the first report concerning PDGFRα, their expression correlates with desmoplasia.

overall_design: We interrogated the database of the Department of Pathology at our Institution and identified seven primary DSRCTs surgically removed after combined chemotherapy between 2000 and 2016. The study was approved by the Independent Ethics Committee of the Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (INT-MI). All of the patients whose biological samples were included in the study gave their signed consent to donate the tissue remaining after the diagnostic procedure had been completed to INT-MI.


title: Genome-wide expression profiling of whole of uhrf1 mutant zebrafish compared to WT siblings at 120 hpf

status: Public on Jul 21 2017

first: Kirsten

last: Sadler Edepli

summary: The goal of this study is to compare gene expression levels in whole uhrf1 mutant larvae to phenotypically normal siblings.

overall_design: Larvae were segregated by phenotype on 5 dpf and 10 larvae with the mutant phenotype and phenotypically normal siblings were pooled.  RNA was extracted. Libraries were prepared according to Illumina Truseq RNA sample prep kit, version 2, followed by Ribo-Zero Gold treatment. Larvae from two separate clutches were analyzed.

first: Yelena

last: Chernyavskaya


title: miR-1199-5p and Zeb1: a novel double-negative feedback coordinating EMT and tumour cell invasion (mRNA-seq)

summary: We investigated the effect of miR-1199-5p, miR-200b-3p and miR-429-3p on gene expression profiles during TGFbeta-induced EMT in normal murine mammary gland cells by using the mRNA-sequencing. Our analysis demonstrates that miR-1199-5p and both miR-200 family members share only 6 target genes, indicating that besides regulating Zeb1 expression they exert distinct functions during EMT.

overall_design: mRNA profiles of NMuMG cells transiently overexpressing miR-1199-5p, miR-200b-3p or miR-429-3p and treated with TGFbeta for 4 days


title: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

first: Bo

last: Wen

summary: Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically；chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. Mechanically, HNRNPU interacts with CTCF and RAD21, which affects the binding of RAD21 to the chromatin significantly, whereas CTCF bindings are almost unchanged, what’ more, the decrease of binding strengths are highly correlated with the weakness of loop bounded by Rad21. Taken together, we identify HNRNPU as a key regulator of chromatin architecture, and our data suggest the importance of nuclear matrix associating factors in 3D genome organization.

overall_design: ChIPseq data of BirA-HNRNPU in AML12 cells

first: Hui

last: Fan

first: Pin

last: Lv


title: Transcriptome of IL-19 negative and IL-19 positive macrophages.

status: Public on Aug 07 2017

summary: RNA-seq analysis of LPS stimulated bone marrow-derived macrophages, derived from heterozygous Il19-tdTomato reporter mice to compare the transcritptome of IL-19/tdTomato negative with IL-19/tdTomato positive macrophages.

overall_design: Differential gene expression profiling of Il19-tdT positive versus negative BM-derived macrophages

first: Anna

last: Steinert

first: Jan

last: Niess

first: Philippe

last: Demougin

first: Florian

last: Geier


title: Comparative expression analysis of the Arabidopsis karrikin (KAR)-receptor mutant, kai2-2, and wild type (WT) plants (Col-0) under dehydration conditions

status: Public on Oct 15 2017

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

summary: To understand the role of KAR-signaling components in water stress response, we have carried out comparative expression analysis of the KAR-receptor kai2-2 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and kai2-2 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Weiqiag

last: Li

first: V

last: Ha

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: L

middle: P

last: Tran


title: Matrix-dependent cardiac progenitor cell fate is instructed by the early regulation of YAP and Plk2

status: Public on Oct 26 2017

first: DBM Bioinformatics

last: Core Facility

summary: Although recent studies support regenerative potential based on cardiac progenitor cells (CPCs), it remains unclear what cues regulate CPC fate. Using 2- and 3D-culture models, we demonstrate that the two most abundantly expressed matrix proteins in the heart, laminin and fibronectin, have opposite roles in CPC fate decision. CPCs on fibronectin showed predominantly nuclear localization of the transcriptional co-activator YAP and maintained proliferation. In contrast, seeding on laminin induced cytosolic retention and degradation of YAP and altered gene expression, which preceded decreased proliferation and enhanced lineage commitment. RNA-sequencing identified Plk2 as candidate target gene of YAP. Plk2 expression depended on YAP stability, was rapidly downregulated on laminin, and its regulation was sufficient to rescue and/or mimic the CPC response to laminin and fibronectin, respectively. These findings propose a novel role of Plk2 and identify an early molecular mechanism in matrix-instructed CPC fate with potential implications for therapeutic cardiac regeneration.

overall_design: Expression profiling of cardiac progenitor cells in suspension and cultured on dishes coated with laminin or fibronectin or on non-coated dishes (biological triplicates each)

first: Michika

last: Mochizuki

first: Robert

last: Ivanek

first: Gabriela

last: Kuster


title: A humanized mouse model to study type 1 diabetes

status: Public on Jul 19 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
The clinical management of type 1 diabetes (T1D) faces the lack of fully predictive biomarkers and of antigen-specific therapies to prevent its development. From a therapeutic standpoint, preclinical modls of T1D have fallen short of directly translating into the human.
To circumvent this limitation, we developed a new mouse model that is deficient for expression of murine major histocompatibility complex class I, class II and of murine insulin genes and instead expresses HLA-A*02:01, the high susceptibility HLA-DQ8 molecule and human insulin.
The metabolic and immune phenotype of these mice is basically identical to that of the parental strains. Upon expression of B7.1 under the control of the rat insulin promoter, these mice develop T1D along with a T-lymphocyte response to human preproinsulin epitopes spanning the whole autoantigen sequence.
This new model will allow evaluating peptide-based immunotherapy that may directly apply to human T1D.

overall_design: We analysed 2 YES mice to compare with one NOD mouse and one C57BL/6 mouse as controls. Finaly, we have 4 samples.

first: LUCE

last: Sandrine

first: GUINOISEAU

last: Sophie

first: LETOURNEUR

last: Franck

first: NITSCHKE

last: Patrick

first: VIDAUD

last: Michel

first: LEMONNIER

last: François

first: BOITARD

last: Christian


title: Diel gene expression analysis of Trichodesmium erythraeum IMS101 in light and dark cycle

status: Public on Jun 11 2017

city: Xiamen

first: Tuo

last: Shi

state: Fujian

address: No. 1 South Xiang'an Rd.

institute: Xiamen University

summary:
Investigation of whole genome gene expression level changes in Trichodesmium erythraeum IMS101 during a 24-hr light and dark cycle.
The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2019. The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). mBio 10:e02495-18. https://doi.org/10.1128/mBio.02495-18.

overall_design: A twenty eight chip study using total RNA extracted from cultures of Trichodesmium erythraeum IMS101 that were harvested at designated time points during a 24-hr diel sampling. Each chip measures the expression level of 4,788 genes from Trichodesmium erythraeum IMS101 with up to six 60-mer probes per gene, with two-fold technical redundancy.

first: Irina

middle: N

last: Shilova


title: Global Transcriptional Profiling of Women Following Roux-en-Y Gastric Bypass

status: Public on Sep 03 2017

city: Ribeirão Preto

first: Marcela

middle: Augusta de Souza

last: Pinhel

state: Sao Paulo

address: Avenida dos Bandeirantes, 3900

department: Internal Medicine

country: Brazil

institute: University of Sao Paulo

summary:
Analysis of changes in gene expression after weight loss.
The hypothesis tested in this study was that the weight loss caused by Roux-en-Y Gastric bypass may alter the expression of genes involved in multiple molecular pathways related to obesity. The results will generate important data for studies involving treatment of obesity, which is characterized as a multifactorial disease that affects thousands of individuals worldwide.

overall_design: Total RNA obtained from peripheral blood mononuclear cells of women with obesity who underwent Roux-en-Y gastric bypass in pre- and postoperative periods (6 months). Women with a normal weight were used as controls.

first: Natália

middle: Y

last: Noronha

first: Carolina

middle: F

last: Nicoletti

first: Bruno

last: Oliveira

first: Driele

last: Quinhoneiro

first: Cristina

last: Cortes-Oliveira

first: Wilson

last: Silva Junior

last: Salgado Junior

first: Julio

last: Marchini

first: Vitor

last: Pinhanelli

first: Carla

middle: B

last: Nonino


title: Development of live-attenuated lymphocytic choriomeningitis virus vectors for potent alarmin-driven CD8+ T cell induction in tumor immunotherapy

status: Public on Mar 08 2017

first: DBM Bioinformatics

last: Core Facility

summary: Effective cancer immunotherapy requires potent tumor antigen-specific effector CD8+ T cell (CTLeff) responses, culminating in an inflammatory activation of the tumor microenvironment. We describe the artificial reengineering of the lymphocytic choriomeningitis virus (LCMV) genome to serve as replication-competent but stably attenuated immunotherapy platform (artLCMV). artLCMV targeted dendritic cells, thereby delivering tumor-associated antigens for efficient CTL induction. Additionally, owing to in vivo spread, artLCMV infected lymphoid tissue stroma expressing interleukin-33, an alarmin released from necrotic cells. Interleukin-33 signals accounted for artLCMV-induced effector CTL responses of higher magnitude and functionality than those induced by replication-deficient LCMV-, adenovirus 5- or vaccinia virus-based vectors. Accordingly, superior immunotherapeutic efficacy of artLCMV in transplantable tumor models depended on interleukin-33 signaling, and massive CTLeff influx was associated with an inflammatory conversion of the tumor. These properties, together with low seroprevalence but excellent immunogenicity of LCMV in humans, suggest artLCMV holds promise as a cancer immunotherapy platform.

overall_design: We implanted EG7-OVA tumor cells subcutaneously into the flank of C57BL/6 mice. On day 7, when tumors became palpable, we treated them with artLCMV-OVA or left them untreated. Tumor tissue was analyzed on d9 after treatment.  Gene expression profiles of inflammation-associated genes from tumor tissue of untreated or artLCMV-OVA treated animals was determined by Nanostring technology. 2 groups (untreated vs artLCMV-OVA), n=4 mice per group.

first: Sandra

last: Kallert

first: Stephanie

last: Darbre

first: Weldy

middle: V

last: Bonilla

first: Mario

last: Kreutzfeldt

first: Nicolas

last: Page

first: Philipp

last: Müller

first: Matthias

last: Kreuzaler

first: Min

last: Lu

first: Stéphanie

last: Favre

first: Max

last: Löhning

first: Sanjiv

last: Luther

first: Alfred

last: Zippelius

first: Doron

last: Merkler

first: Daniel

middle: D

last: Pinschewer


title: Analysis of cord blood B cells

status: Public on Mar 01 2017

first: Richard

last: Lo-Man

address: 25-28 Rue du Docteur Roux

institute: Institut Pasteur

summary: Purified CD19+ B cells isolated from the cord blood were purified in subsets and activated by diferent stimuli and compared by whole genome microarray analysis.

overall_design: Neonatal B cell were isolated as CD19+CD3negativeCD5+CD10negative and activated by anti-IgM, R848, RSV or Influenza virus

first: Sebastien

last: Lemoine


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Junguk6-2)

status: Public on Apr 26 2017

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

summary: To understand the drought stress induced signaling mechanism in trees.

overall_design: 10min air-dried treatment to plant, Transcriptome profiling

first: Bong-Gyu

last: Mun

first: Hyun-Ho

last: Kim

first: Jae-Young

first: Adil

last: Hussain

first: Byung-Wook

last: Yun


title: Expression data from yeasts under non-caloric restriction (NR), caloric restriction (CR) and rapamycin treatment (RM)

status: Public on Jun 30 2017

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: We performed microarrays to identify change of gene expression under NR, CR, and RM and found differentially expressed genes between each condition.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We harvested yeast cells under each condition at day 5 after inoculation.  Microarray was performed in biological triplicate on cells under NR, CR and RM.

first: Cheol-Koo


title: Secondary proteasome inhibitor carfilzomib resistant myeloma cell lines

status: Public on Oct 09 2016

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Modulation of the activity of the ubiquitin-proteasome pathway with the proteasome inhibitor (PI)  is an established component of therapy for plasma cell disorders. However, resistance emerges and the mechanism is incompletely understood. We generated carfilzomib-resistant (CR) myeloma cell lines by exposing drug-naive ANBL-6, KAS-6/1, U266, and OPM-2 cells to increasing concentrations of carfilzomib and then performed gene expression profiling (GEP) to identify prominent changes compared to their vehicle-treated counterparts, followed by exploration of the mechanism(s) of proteasome inhibitor resistance.

overall_design: We generated carfilzomib-resistant (CR) myeloma cell lines by exposing drug-naive ANBL-6, KAS-6/1, U266, and OPM-2 cells to increasing concentrations of carfilzomib.  These were then subjected to gene expression profiling (GEP) to identify prominent changes compared to their vehicle-treated counterparts.

first: Huihan

last: Wang

first: Bingzong

last: Li

first: Zhiqiang

first: R

last: Davis

first: Robert

middle: Z

last: Orlowski


title: A HAND2 Cistrome Controls Heart Development and the Endothelial-Mesenchymal Transition during Cardiac Valve Formation

status: Public on May 24 2017

first: DBM Bioinformatics

last: Core Facility

summary: Our analysis identifies the direct transcriptional targets of HAND2 in mouse embryonic hearts, both ih second heart field derived structures and in the formation of the cardiac cushions

overall_design: ChIP-Seq analysis using a Hand2-3xFlag allele on dissected E10.5 cardiac embryonic tissues

first: Frédéric

last: Laurent

last: Ivanek

first: Rolf

last: Zeller


title: AML associated oncofusion proteins PML-RARA, AML1-ETO and CBFB-MYH11 target RUNX/ETS-factor binding sites to modulate H3ac levels and drive leukemogenesis

status: Public on Nov 22 2016

first: Joost

last: Martens

institute: Radboud University

summary: Chromosomal translocations are one of the hallmarks of acute myeloid leukemia (AML), often leading to gene fusions and expression of an oncofusion protein. Over recent years it has become clear that most of the AML associated oncofusion proteins molecularly adopt distinct mechanisms for inducing leukemogenesis. Still these unique molecular properties of the chimeric proteins converge and give rise to a common pathogenic molecular mechanism. In the present study we compared genome-wide DNA binding and transcriptome data associated with AML1-ETO, CBFB-MYH11 and PML-RARA oncofusion protein expression (GSE46044, GSE23730, GSE30254 and GSE18886) to identify unique and common features. Our analyses revealed targeting of oncofusion binding sites to RUNX1 and ETS-factor occupied genomic regions. In addition, it revealed highly similar expression of common target genes and specific enrichment of several biological pathways critical for maintenance of AML, suggesting oncofusion proteins deregulate common gene programs despite their distinct binding signatures and mechanisms of action.

overall_design:
ChIP-seq profiling of RUNX1 in NB4 cells
Abhishek ,Singh

first: Amit

last: Mandoli

first: Koen

last: Prange

middle: H


title: Human iPSC glial mouse chimeras reveal glial contributions to schizophrenia

status: Public on Jul 20 2017

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Genetic studies have suggested a role for glial pathology in the genesis of schizophrenia (SCZ).  To assess the nature of SCZ-associated human glial dysfunction in vivo, we established human glial chimeric mice using glial progenitor cells (GPCs) produced from induced pluripotential cells (hiPSCs), derived from patients with juvenile-onset schizophrenia or healthy controls. To this end, hiPSC GPCs were implanted neonatally into either immunodeficient myelin wild-type mice, in which donor GPCs remained as progenitors or became astrocytes, or into myelin-deficient shiverer mice, in which the GPCs also gave rise to oligodendrocytes. When implanted into shiverers, the SCZ-derived GPCs exhibited less expansion in the white matter than did control GPCs, instead migrating prematurely into the cortex. The SCZ GPC-transplanted shiverers were consequently hypomyelinated relative to control GPC-engrafted mice. When established instead in myelin wild-type hosts, the SCZ hiPSC glial chimeras manifested markedly delayed and diminished astrocytic differentiation, which was associated with diminished prepulse inhibition and an aberrant behavioral phenotype across multiple modalities. Accordingly, RNA-seq revealed significant differences in both glial differentiation-associated and synaptic gene expression by SCZ GPCs. These data suggest a potent contribution of cell-autonomous glial dysfunction to the development of schizophrenia, and provide a model for the in vivo assessment of human glial pathology in this disorder.

overall_design: mRNA was isolated by polyA-selection protocol from FACS-sorted PDGFRa-positive GPC cell lines produced from iPS cells derived from 4 schizophrenic patients (designated to SCZ lines 8 [N = 4 independent cell preparations], 29 [N = 3], 51 [N = 7], and 164 [N = 8]) and 3 healthy controls (designated to CTR lines 22 [N = 3], 37 [N = 4], and 205 [N = 7]). FASTQ files in the submission were edited by Trimmomatic. The software was used to trim adapter sequences and low-quality bases (see processing steps). The overall file structure and format remained unchanged. The count matrix in the submission is as obtained directly from featureCounts tool, that is, no manipulation was performed to the count data. The data normalization was performed internally in the analysis and the raw count data was used in differential expression analysis. Please refer to the Materials and Methods section in supplementary files. The complete reproducible workflow, including R scripts, sample information sheet, and count matrix, was deposited to https://github.com/cbtncph/GoldmanetalSCZ2016

first: Martha

last: Windrem

first: Mikhail

last: Osipovitch

first: Su

first: Janna

last: Bates

first: Lisa

last: Zou

first: Zhengshan

last: Liu

first: Jared

last: Munir

first: Devin

last: Chandler-Militello

last: Miller

first: Maiken

last: Nedergaard

last: Findling

first: Paul

last: Tesar


title: REPARATION:  Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes

status: Public on Jan 30 2017

city: Gent

first: Petra

last: Damme

state: East Flanders

address: Albert Baertsoenkaai 3

department: Department of Biochemistry

country: Belgium

institute: University of Gent

summary: The delineation of genes in bacteria has remained an important challenge because prokaryotic genomes are often tightly packed frequently resulting in overlapping genes. We hereby present a de novo approach called REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION) to delineate translated open reading frames (ORFs) in bacteria independent of (available) genome annotation. By deep sequencing of ribosome protected mRNA fragments (RPF) to map translating ribosomes across the entire genome, REPARATION takes advantage of the recently developed ribosome profiling (Ribo-seq) technique. REPARATION starts by traversing the entire genome to generate all possible ORFs and then collects their corresponding RPF signal information. Based on a growth curve model to estimate minimum ORF read density and Ribo-seq RPF coverage, thresholds indicative of translation is estimated. Finally, our algorithm applies a random forest model to build a classifier to classify putative protein coding ORFs. We evaluated the performance of REPARATION on 3 annotated bacterial species using in-house generated Ribo-seq data and matching N-terminal and shotgun proteomics data next to publically available Ribo-seq data. In all cases, about 80% of the ORFs predicted by REPARATION were previously annotated as protein coding. While 13-20% were variants of previously annotated ORFs and about 3-4% point to novel translated ORFs within intergenic or other regions previously annotated as non-coding. Without stringent length restrictions REPARATION was able to identify several small ORFs (sORFs). Multiple supportive evidence from matching MS data and sequence conservation analysis was obtained to validate predicted ORFs.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Ribosome profiling and mRNA sequencing of monosome and polysome-enriched samples of Salmonella enterica serovar Typhimurium - strain SL1344.

first: Elvis

last: Ndah

first: Veronique

last: Jonckheere

first: Adam

last: Giess

first: Eivind

last: Valen

first: Gerben

last: Menschaert

last: Van Damme


title: Type-I-Interferons induce the decimation of antiviral B cells at the onset of chronic infection

status: Public on Sep 19 2016

first: DBM Bioinformatics

last: Core Facility

institute: University of Basel

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Epigenetic regulation of the apoptosis program in t(8;21) AMLs by an AML1-ETO, ERG and RUNX1 triad

status: Public on Nov 15 2016

first: Joost

last: Martens

summary: The t(8;21) acute myeloid leukemia associated oncoprotein AML1-ETO is a transcription factor that aberrantly regulates the pathways that lead to myeloid differentiation. Here, we set out to investigate the effects of AML1-ETO on gene expression and the epigenome in patient blast cells. We identify two modules, one in which AML1-ETO binds promoter regions of active genes and one represented by non-promoter binding to accessible, yet inactive chromatin regions. Using genome-wide binding analysis and mass spectrometry interaction studies we identify ERG, FLI1, TAL1 and RUNX1 as common binding factors of all AML1-ETO occupied genomic regions, while LYL1 and LMO2 show preferential binding in the context of non promoter regions. Epigenetically, reduced histone acetylation levels at non-promoter regions seems HDAC dependent, as treatment with an HDACi increases acetylation and induces cell death. Both AML1-ETO modules are represented in most aberrantly regulated pathways, including many signaling pathways, self-renewal and apoptosis. For the latter, the expression of the wild type transcription factors RUNX1 and ERG is required, as alterations in expression are associated with the onset of an apoptosis program. Interestingly, upon RUNX1 or ERG knockdown this onset seems to be dependent on increased AML1-ETO expression as combinatorial knockdown of RUNX1/AML1-ETO or ERG/AML1-ETO results in rescue from apoptosis. Together our results show that the balanced interplay of the epigenetic environment and transcription factors retains an anti apoptotic phenotype in t(8;21) AML cells.

overall_design: 14 samples for ChIP seq and 2 RNA-seq samples

first: Amit

last: Mandoli

first: Abhishek

last: Singh

first: Marjolein

last: Oerlemans

first: Rene

last: Dirks

first: Koen

last: Prange

first: Menno

middle: T

last: Huurne

first: Bart-Jan

last: Wierenga

first: Eva

last: Janssen-Megens

first: Kim

last: Berentsen

first: Nilofar

last: Sharifi

first: Bowon

last: Kim

first: Filomena

last: Matarese

first: Luan

last: Nguyen

first: Nina

middle: C

last: Hubner

first: Nagesha

last: Rao

first: Lucia

last: Altucci

first: Edo

last: Vellenga

first: Hendrik

last: Stunnenberg


title: Type-I-Interferons induce the decimation of antiviral B cells at the onset of chronic infection [RNA-seq]

first: DBM Bioinformatics

last: Core Facility

summary:
Abstract: Immune subversion represents a hallmark of persistent infection, but microbial suppression of B cell responses remains mechanistically ill-defined.
Adoptive transfer experiments in a chronic viral infection model evidenced the rapid and profound decimation of B cells that responded to virus or to concomitantly administered protein. Decimation affected naïve and memory B cells and resulted from biased differentiation into short-lived antibody-secreting cells. It was driven by type I interferon (IFN-I) signaling to several cell types including dendritic cells, T cells and myeloid cells. Durable B cell responses were restored upon IFN-I receptor blockade or, partially, when depleting myeloid cells or key IFN-I-induced cytokines.
B cell decimation represents a molecular mechanism of humoral immune subversion and reflects an unsustainable “all-in” response of B cells in IFN-I-driven inflammation.

overall_design: We adoptively transferred naïve KL25HL cells (LCMV-WE-GP-specific B cells) to αIFNAR- or isotype control-treated syngeneic recipient mice, followed by rLCMV-Cl13/WE-GP. On day 3 of infection, spleen were harvested and proliferated KL25HL B cell progeny (CD45.1+B220+CFSElo) were FACS-sorted and total RNA was processed for RNAseq. n=4

first: Florian

last: Geier

first: Benedict

last: Fallet

first: Daniel

last: Pinschewer

first: Kerstin

last: Narr

first: Yusuf

middle: I

last: Ertuna

first: Melissa

last: Remy

first: Rami

last: Sommerstein

first: Karen

last: Cornille

first: Mario

last: Kreutzfeldt

first: Nicolas

last: Page

first: Tobias

last: Straub

first: Hanspeter

last: Pircher

first: Kevin

last: Larimore

first: Philipp

last: Greenberg

first: Doron

last: Merkler

first: Gert

last: Zimmer

first: Danny

last: Labes

first: Gabriela

last: Salinas

first: Susanne

last: Luthin

first: Fabian

last: Ludewig

first: Thomas

last: Lingner


title: UGA Folate and Pregnancy

status: Public on Apr 19 2016

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

type: Methylation profiling by genome tiling array

summary: Umbilical cord blood was collected from live deliveries at the Athens Regional Midwifery Clinic. Neonatal sex, race and gestational age was obtained by review of the delivery records.

overall_design: Bisulfite converted DNA from 24 cord blood samples collected at delivery was hybridized to the Illumina HumanMethylation450 BeadChip.

first: Lynn

last: Bailey

first: Hea

last: Park


title: Type-I-Interferons induce the decimation of antiviral B cells at the onset of chronic infection [nanostring]

city: Basel

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

summary:
Abstract: Immune subversion represents a hallmark of persistent infection, but microbial suppression of B cell responses remains mechanistically ill-defined.
Adoptive transfer experiments in a chronic viral infection model evidenced the rapid and profound decimation of B cells that responded to virus or to concomitantly administered protein. Decimation affected naïve and memory B cells and resulted from biased differentiation into short-lived antibody-secreting cells. It was driven by type I interferon (IFN-I) signaling to several cell types including dendritic cells, T cells and myeloid cells. Durable B cell responses were restored upon IFN-I receptor blockade or, partially, when depleting myeloid cells or key IFN-I-induced cytokines.

overall_design: We transferred KL25HL cells (LCMV-WE-GP-specicifc B cells) into wt recipients, treated with αGR-1 (myeloid cell depletion, n=3), αIFNAR (IFN-I recpetor blockade, n=3) or control antibody (n=4), followed by rCl13 infection. Additional animals were left uninfected (n=2)). On day 3 we processed spleen and BM for low-density expression profiling of 248 inflammatory genes using the nCounter Nanostring Mouse Inflammation v2 assay (NanoString Technologies).

first: Florian

last: Geier

first: Benedict

last: Fallet

first: Daniel

last: Pinschewer

first: Kerstin

last: Narr

first: Yusuf

last: Ertuna

first: Melissa

last: Remy

first: Rami

last: Sommerstein

first: Karen

last: Cornille

first: Didier

last: Chollet


title: Next Generation Sequencing of long-term hematopoietic cells (LT-HSCs) with or without mutations in JAK2 and Ezh2

status: Public on Jun 24 2016

summary:
Comparison of mRNA expression profiles of LT-HSCs with or without mutations in JAK2 and Ezh2 by RNA sequencing.
LT-HSC mRNA was extracted from six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) 10 weeks after tamoxifen injection.
Our study represents the first detailed analysis of mRNA expression profile of LT-HSC with or without mutations in JAK2 and Ezh2 , with biologic replicates, generated by RNA-seq technology. Our results revealed that mRNA expression profile of LT-HSC with different genotype showed specific gene expression patterns, which allows to do biological comprehensive and quantitative analysis for hematopoiesis.

overall_design: LT-HSCs mRNA profiles six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) were generated by deep sequencing.

first: Takafumi

last: Shimizu

first: Robert

last: Ivanek

first: Radek

last: Skoda


title: Victorian Infant Collaborative Study

status: Public on Apr 18 2016

summary: DNA samples were derived from dried blood spots taken for newborn screening when infants were several days of age, after obtaining permission from the participants when they were aged 18 years, or from their parents if they were younger than 18 years.

overall_design: 298 survivors born either <1000 g or <28 weeks’ gestation in the state of Victoria were enrolled in a longitudinal follow-up study, which was approved by the Human Research Ethics Committees at the Royal Women’s Hospital, the Mercy Hospital for Women, Monash Medical Centre, and the Royal Children’s Hospital, Melbourne, Australia.  Gestational age was determined by ultrasound estimation before 20 weeks of gestation, or by menstrual history in the minority if no ultrasound dating was available.

first: Lex

last: Doyle

first: Jeanie

last: Chong

first: Jeff

last: Craig


title: Loss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosis


title: Genome-wide occupancy of Tcf7l2/Tcf4 in rat and expression profiling of Tcf7l2 mutant and control mice

status: Public on Feb 19 2016

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Next Generation Sequencing of megakaryocyte-erythrocyte progenitor cells (MEPs) with or without mutations in JAK2 and Ezh2

first: DBM Bioinformatics

last: Core Facility

summary:
Comparison of mRNA expression profiles of MEPs with or without mutations in JAK2 and Ezh2 by RNA sequencing.
MEPs mRNA was extracted from six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) 10 weeks after tamoxifen injection.
Our study represents the first detailed analysis of mRNA expression profile of MEP with or without mutations in JAK2 and Ezh2 , with biologic replicates, generated by RNA-seq technology. Our results revealed that mRNA expression profile of MEP with different genotype showed specific gene expression patterns, which allows to do biological comprehensive and quantitative analysis for hematopoiesis.

overall_design: MEPs mRNA profiles six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) were generated by deep sequencing.


title: Bioreactor-engineered cancer tissues mimic phenotypes, gene expression profiles and drug resistance mechanisms detectable in xenografts and clinical specimens.

status: Public on Jan 25 2016

summary: Cancer tissue-like structures were developed by using established human tumor cell lines in perfusion-based bioreactor systems. In colorectal cancer (CRC) cell lines, perfusion allowed more homogeneous scaffold seeding than tri-dimensional (3D) static cultures and significantly (13.7 fold, p<0.0001) higher proliferation. Resulting tissues exhibited morphology and phenotypes similar to xenografts generated in immunodeficient mice. Whole transcriptome analysis of 2D, 3D static and 3D perfusion cultures revealed the highest correlation between xenografts and 3D perfusion cultures (r=0.985). Clinically relevant concentrations of 5-FU, used in neo- and adjuvant CRC treatment, had no effect on numbers of HT-29 CRC cells cultured in 3D perfusion or xenografts, as compared with a 55.8% reduction in 2D cultures. Treatment induced apoptosis in 2D cultures, but only “nucleolar stress” in perfused cells and xenografts, consistent with partial responsiveness.  In 3D perfusion cultures BCL-2, TRAF1, and FLIP gene expression was marginally affected, as compared with significant down-regulation in 2D cell cultures. Accordingly, ABT-199 BCL-2 inhibitor, induced cytostatic effects in 3D perfusion but not in 2D cell cultures (p=0.003). Tumor cells from partially responsive (Dworak 2) patients undergoing neo-adjuvant treatment, typically (10/11) expressed BCL-2, as compared with 0/3 highly (Dworak 3-4) responsive and 4/15 fully resistant CRC (Dworak 0/1, p=0.03), closely matching 3D perfusion cultures data. These results indicate that 3D perfusion cultures efficiently mimic phenotypic and functional features observed in xenografts and clinical specimens. These models may be of critical translational relevance to address fundamental human tumor cell biology issues and to develop predictive pre-clinical tests of novel compounds.

overall_design: Expression profiles of colorectal cancer cell lines cultured in 2D, 3D static, 3D perfusion or growing as xenografts were generated by deep sequencing, in triplicates, using Illumina HiSeq2000.

first: Christian

last: Hirt

first: Muraro

middle: G

last: Manuele

first: Mele

last: Valentina

first: Ivan

last: Martin

first: Giulio

last: Spagnoli


title: Genome-wide maps of Wnt effector Tcf7l2/Tcf4 occupancy in oligodendrocyte during CNS myelination

summary: We performed genome-wide profiling of Tcf7l2 occupancy during oligodendrocyte differentiation and identified the  key enzymes involved in cholesterol metabolism and essential for CNS myelination.

overall_design: Examination of Tcf7l2 chIP-seq in oligodendrocyte progenitor cell and 2 differentiation oligodendrocytes.

first: Chuntao

last: Zhao


title: Antibody-induced CD47 signaling suppresses triple-negative breast cancer stem cells

status: Public on Apr 01 2016

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary:
Intercellular communication is critical for integrating complex signals in multicellular eukaryotes.  Vascular endothelial cells and T lymphocytes closely interact during the recirculation and trans-endothelial migration of T cells.  In addition to direct cell-cell contact, we show that T cell derived extracellular vesicles can interact with endothelial cells and modulate their cellular functions.  Thrombospondin-1 and its receptor CD47 are expressed on exosomes/ectosomes derived from T cells, and these extracellular vesicles are internalized and modulate signaling in both T cells and endothelial cells.  Extracellular vesicles released from cells expressing or lacking CD47 differentially regulate activation of T cells induced by engaging the T cell receptor.   Similarly, T cell-derived extracellular vesicles modulate endothelial cell responses to vascular endothelial growth factor and tube formation in a CD47-dependent manner. Uptake of T cell derived extracellular vesicles by recipient endothelial cells globally alters gene expression in a CD47-dependent manner. CD47 also regulates the mRNA content of extracellular vesicles in a manner consistent with some of the resulting alterations in target endothelial cell gene expression. Therefore, the thrombospondin-1 receptor CD47 directly or indirectly regulates intercellular communication mediated by the transfer of extracellular vesicles between vascular cells.
Treatment with B6H12 antibody inhibited co-immunoprecipitation of EGFR with CD47 and inhibited EGF-induced EGFR tyrosine phosphorylation. B6H12 treatment of bCSC also suppressed asymmetric cell division and cell proliferation and up-regulated caspase 3/7 activity.  Correspondingly, caspase-7 cleavage in human breast cancers correlated with CD47 expression. Our data shows that B6H12 specifically targets bCSCs but not differentiated cancer cells, and this CD47 signaling is independent of SIRPα.  Three replicates of each condition were generated.

overall_design: Three replicates of each MDA-231 attached cells (differentiated), MDA-231 in suspension cells (bCSC), MDA-231 in suspension cells (bCSC) treated with Control Antibody and MDA-231 in suspension cells (bCSC) treated with B6H12 Antibody.

first: A

first: Sukhbir

last: Kaur

first: David

last: Roberts


title: The MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in MLLr AML

status: Public on Jan 24 2017

city: Nijmegen

first: Joost

last: Martens

address: Geert Grooteplein 28

summary: In MLL-rearranged (MLLr) leukemias the N terminal part of the MLL gene can be fused to over 60 different partner genes. Here, we investigate the genome wide binding of the MLL-AF9 and MLL-AF4 fusion proteins and their epigenetic signatures in order to define a core set of MLLr targets. We uncover both common as well as specific MLL-AF9 and MLL-AF4 target genes, which are all marked by H3K79me2, H3K27ac, and H3K4me3. Apart from promoter binding, we also identify MLL-AF9 and MLL-AF4 binding at specific subsets of non overlapping active distal regulatory elements. Despite this differential enhancer binding MLL-AF9 and MLL-AF4 still share a common gene program, which represents part of the RUNX1 gene program and constitutes of CD34+ and monocyte specific genes. Comparing these datasets revealed several zinc finger transcription factors as potential MLL-AF9 co-regulators. Together these results suggest that MLL-fusions collaborate with specific subsets of TFs to aberrantly regulate the RUNX1 gene program in 11q23 AMLs.

overall_design: Genome-wide (ChIP-seq) binding of MLL, AF9, AF4, H3K4me3, H3K27ac, H3K79me2 and RUNX1 in THP-1 and MV4-11 AML cell lines. Expression Profiling (RNA-seq) of THP-1 and MV4-11 cell lines, as well as 5 MLL-AF9 positive patient blasts.

first: Koen

middle: M

last: Prange

first: Amit

last: Mandoli

first: Tatyana

last: Kuznetsova

first: Shuang-Yin

last: Wang

first: Ana

last: Sotoca

first: Anna

middle: E

last: Marneth

first: Bert

middle: A

last: van der Reijden

first: Hendrik

last: Stunnenberg


title: Expression data from murine brain tumors

status: Public on Dec 03 2015

first: DBM Bioinformatics

last: Core Facility

summary:
There is evidence that brain tumor cells may hijack self-renewal mechanism that regulate stem cell maintenance during normal development. Notch signaling is fundamental for maintaining normal neural stem cells in an undifferentiated state and has been implicated in in the maintenance of brain tumor stem cells as well.
We used microarrays to detail the global gene expression program in murine brain tumors lacking RBPjk, an indispensable mediator of the Notch signaling pathway in the cell nucleus.

overall_design: PDGF+p53-/- tumors were induced in p53 floxed mice by combined over-expression of PDGF-B and Cre-recombinase (Cre) from a PDGF-IRES-Cre retroviral construct. PDGF-gain and p53 loss simulate mutations found in human glioblastoma. PDGF+p53-/-RBPjk-/- tumors were induced with the PDGF-IRES-Cre retrovirus in mice carrying floxed p53 and RBPjk alleles. p53-/-RBPjk-/- tumors were induced by conditional deletion of floxed p53 and RBPjk alleles in Hes5+ cells using an Hes5::CreERT2 transgenic mouse line.

first: Claudio

last: Giachino

first: Robert

last: Ivanek

first: Verdon

last: Taylor


title: miR-1199-5p and Zeb1: a novel double-negative feedback coordinating EMT and tumour cell invasion

status: Public on Nov 09 2017


title: miR-23~27~24 clusters control effector T cell differentiation and function

status: Public on Dec 11 2015

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

summary: Coordinated repression of gene expression by evolutionarily conserved microRNA (miRNA) clusters and paralogs ensures that miRNAs efficiently exert their biological impact. Combining both loss- and gain-of-function genetic approaches, here we show that the miR-23~27~24 clusters regulate multiple aspects of T cell biology, particularly Th2 immunity. Low expression of this miRNA family confers proper effector T cell function at both physiological and pathological settings. Further studies in T cells with exaggerated regulation by individual members of the miR-23~27~24 clusters revealed miR-24 and miR-27 collaboratively limit Th2 responses through targeting IL-4 and GATA3 in both direct and indirect manners. Intriguingly, while overexpression of the entire miR-23 cluster also negatively impacts other Th lineages, enforced expression of miR-24, in contrast to miR-23 and miR-27, actually promotes the differentiation of Th1, Th17 and iTreg cells, implying that under certain conditions, miRNA families can fine tune the biological effects of their regulation by having individual members antagonize rather than cooperate with each other. Together, our results identify a miRNA family with important immunological roles and suggest tight regulation of miR-23~27~24 clusters in T cells is required to maintain optimal effector function and to prevent aberrant immune responses.

overall_design: naïve T cells isolated from mice with T cell-specific overexpression of the entire miR-23 cluster or individual miR-23 family members as well as from mice with T cell-specific deletion of both miR-23a/b clusters

first: Sunglim

last: Cho

first: Cheng-Jang

last: Wu

first: Tomoharu

last: Yasuda

first: Leilani

middle: O

last: Cruz

first: Ling-Li

last: Lin

first: Duc

last: Nguyen

first: Marina

last: Miller

first: Hyang-Mi

last: Lee

first: Ming-Ling

last: Kuo

last: Broide

first: Klaus

last: Rajewsky

first: Alexander

last: Rudensky

first: Li-Fan

last: Lu


title: Next generation sequencing facilitates quantitative analysis of control of Candida albicans ATCC 10231 and garlic oil-treated C. albicans ATCC 10231 transcriptomes

status: Public on Jul 07 2015

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of C. albicans ATCC 10231 (RNA-seq) to transcriptome profiling of garlic oil-treated C. albicans ATCC 10231 and to evaluate protocols for optimal high-throughput data analysis
Methods:SDB medium, C. albicans cells and garlic oil were added to two separate 50 mL conical flasks. The initial cell concentrations in culture were both 105 CFU/mL. The cultures were incubated in a water bath shaker at 28 ºC with shaking at 150 rpm for 12 h. Garlic oil or PBS buffer were then added to the cultures to make the concentrations of garlic oil arrived at 0 (control) and 1.25 μl/mL, respectively. The cultures were continuously incubated at the same conditions for 5 h. The cells were then sampled and centrifuged. The cell precipitates in the control and 1.25 μl/mL garlic oil groups were quickly separately frozen at -80 ºC. Then total RNA were repared from the cell pellets.
Results:The RNA sequencing results showed that many genes in C. albicans exposed to garlic oil were differentially expressed. Nearly three thousand genes were differentially expressed, with either an increase or decrease of more than twofold. Most of them were down regulated  while a small number were upregulated.
Conclusions: Our study indicated that garlic oil induced differential expression of some critical genes, such as genes for cellular response to drugs, oxidation-reduction processes, pathogenesis, and the cellular response to starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, such as oxidative phosphorylation, spliceosome, cell cycle, protein processing in endoplasmic reticulum, pyrimidine metabolism, meiosis, RNA transport, ribosome biogenesis, and RNA degradation.

overall_design: The mRNA profiles of C. albicans ATCC 10231 (ck) and garlic oil-treated C. albicans ATCC 10231 (sample1) were generated by deep sequencing, in one time, using Illumina Higseq 2500.

first: Zhi-Qiang

last: Huang

first: Wen-Ru


title: Streptococcus gallolyticus modulates phase I biotransformation enzymes in colorectal cancer cells through the aryl hydrocarbon receptor.

status: Public on Jun 01 2015

first: Annemarie

last: Boleij

address: Geert Grooteplein 10

institute: Radboud University Nijmegen Medical Centre

summary:
The opportunistic pathogen Streptococcus gallolyticus is one of the few intestinal bacteria that has been consistently linked to colorectal cancer (CRC). This study aimed to identify S. gallolyticus-induced  pathways that could on the long-term add to CRC progression. Transcription profiling of S. gallolyticus-exposed CRC-cells revealed the persistent induction of enzymes involved in biotransformation pathways. Specifically, a diffusible factor of S. gallolyticus (SGF-X) interacts with the aryl hydrocarbon receptor thereby inducing CYP1 enzymes that catalyze the bioactivation of polycyclic aromatic hydrocarbons (PAHs) into toxic intermediates. Importantly, priming CRC-cells with SGF-X containing medium increased the DNA damaging effect of the PAH 3-methylcholanthrene, which was not observed for other intestinal bacteria. In conclusion, this study shows for the first time that bacteria can modulate the biotransformation capacity of CRC-cells that offers a novel theory for a contributing role of S. gallolyticus in the etiology of sporadic CRC.
Key words : Colorectal cancer cells, Streptococcus bovis, streptococcus gallolyticus, host-pathogen interactions, Cytochrome P4501A1, DNA-damage, polycyclic aromatic hydrocarbons

overall_design: Expression patterns of colorectal cancer cells co cultured with S. gallolyticus, E. faecalis and S. macedonicus were compared with colorectal cancer cells that were not exposed to these bacteria. We find that S. gallolyticus induced oxidoreductase gene pathways. This was validated with in vitro Q-PCR and functional analysis showing that these genes were also altered in other colorectal cancer cell lines and that his effect was translated to the functional level.

first: Rian

last: Roelofs

first: Wilber

last: Peters

first: Dorine

middle: W

last: Swinkels

first: Harold

last: Tjalsma

first: Joris

last: Veltman

first: Christian

last: Gilissen


title: Growth cone localization of the mRNA encoding a chromatin regulator modulates neurite outgrowth

status: Public on Mar 26 2015

first: DBM Bioinformatics

last: Core Facility

summary: Neurons exploit mRNA localization and local translation to spatio-temporally regulate gene expression during development. Local translation and retrograde transport of transcription factors regulate nuclear gene expression in response to signaling events at distal neuronal ends. Whether epigenetic factors could also be involved in such regulation is not known. We report that the mRNA encoding the high mobility group N5 (HMGN5) chromatin binding protein localizes to growth cones of both neuronal-like cells and of hippocampal neurons. We show that Hmgn5 3’UTR drives growth cone localization and translation of a reporter gene, and that HMGN5 can be retrogradely transported into the nucleus along neurites. Loss of HMGN5 function induces transcriptional changes and impairs neurite outgrowth while HMGN5 overexpression induces neurite outgrowth and global chromatin decompaction. Interestingly, control of both neurite outgrowth and chromatin structure is dependent on proper growth cone localization of Hmgn5 mRNA. Our results provide the first evidence that mRNA localization and local translation might serve as a mechanism to couple the dynamic neuronal outgrowth process with chromatin regulation in the nucleus.

overall_design: N1E-115 mouse neuroblastoma cells were transfected with control siRNAs or with siRNAs against Hmgn5. They were then allowed to differentiate and extend neurites for 4h or 24h. Total RNA was then extracted and subjected to microarray analysis.

first: Francesca

last: Moretti

first: Robert

last: Ivanek

first: Olivier

last: Pertz


title: ImmGen ATAC-seq data

status: Public on Jul 04 2017

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Immunological Genome Project chromatin accessibility maps for 86 different immunocytes (ATAC-seq).  Immune cell populations were isolated in high-purity by flow cytometry.

overall_design:
Immune cell populations encompassing all major lineages were isolated by flow cytometry to high-purity according to ImmGen SOP (https://www.immgen.org/). 10,000 cells (except some rare cell populations) were used to construct each ATAC-seq library, using the Fast-ATAC protocol. Libraries were dual-indexed and pooled for high-throughput sequencing.
Highly purified cell samples were isolated in parallel from the same populations for gene expression profiling by low-input RNAseq (ImmGen protocol, per umbrella GSE126267). These corresponding RNAseq datasets are available at GSE109125.
--------------------------------------
Immunological Genome Project Consortium

first: Hideyuki

last: Yoshida

first: Ricardo

last: Ramirez

first: Caleb

last: Lareau

first: Jason

last: Buenrostro

first: Andrew

last: Rhoads

first: Sara

last: Mostafavi

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: EpiPrem Study

status: Public on Apr 07 2016

first: Alicia

last: Smith

summary: Longitudinal samples were collected from neonates in the NICU at the Royal Women’s Hospital in Melbourne, Australia. Blood collection occurred by heel stick and was collected on Whatman paper shortly after birth at 25 weeks gestation, one day post birth, and at the equivalent of 28, 32, 36, and 40 weeks gestation.

overall_design: DNA methylation was assessed in whole blood taken from 2 samples. DNA was extracted using the DNeasy Kit (Qiagen). DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).

first: Christiane

last: Theda

first: Jeff

last: Craig


title: Analysis of mRNA profiles distinguishes proneural (PN) glioma stem cells (GSC) from mesenchymal (Mes) GSCs

status: Public on Mar 20 2015

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: Tumor heterogeneity of high-grade glioma (HGG) is recognized by four clinically relevant subtypes based on core gene signatures. However, molecular signaling in glioma stem cells (GSCs) in individual HGG subtypes is poorly characterized. Here we identified and characterized two mutually exclusive GSC subtypes with distinct dysregulated signaling pathways. Analysis of mRNA profiles distinguished proneural (PN) from mesenchymal (Mes) GSCs and revealed a pronounced correlation with the corresponding PN or Mes HGGs. Mes GSCs displayed more aggressive phenotypes in vitro and as intracranial xenografts in mice. Further, Mes GSCs were markedly resistant to radiation compared with PN GSCs. The glycolytic pathway, comprising aldehyde dehydrogenase (ALDH) family genes and in particular ALDH1A3, were enriched in Mes GSCs. Glycolytic activity and ALDH activity were significantly elevated in Mes GSCs but not in PN GSCs. Expression of ALDH1A3 was also increased in clinical HGG compared with low-grade glioma or normal brain tissue. Moreover, inhibition of ALDH1A3 attenuated the growth of Mes but not PN GSCs. Last, radiation treatment of PN GSCs up-regulated Mes-associated markers and downregulated PN-associated markers, whereas inhibition of ALDH1A3 attenuated an irradiation-induced gain of Mes identity in PN GSCs. Taken together, our data suggest that two subtypes of GSCs, harboring distinct metabolic signaling pathways, represent intertumoral glioma heterogeneity and highlight previously unidentified roles of ALDH1A3-associated signaling that promotes aberrant proliferation of Mes HGGs and GSCs. Inhibition of ALDH1A3- mediated pathways therefore might provide a promising therapeutic approach for a subset of HGGs with the Mes signature.

overall_design: HGG tumors are composed of heterogeneous tumor cell populations including glioma stem cells (GSC) which may contribute to the therapeutic resistance of HGG. GSCs were derived from 19 high-grade glioma (HGG) samples and a fetal neural progenitor (16wf). We observed two phenotypically different GSC cultures with distinct morphologies. One set of GSC cultures (n = 10) displayed round neurosphere-like floating aggregates (cluster 1), and the other set (n = 9) formed irregular-shaped floating aggregates with some adherent cells on the bottom of the culture dish (cluster 2). Cluster 2 GSCs showed more aggressive phenotypes than cluster 1 GSCs in vitro and in vivo. We performed transcriptome microarray analysis of 27 GSC samples (triplicate samples) from nine patient-derived GSC cultures, five glioma cell lines as well as normal human astrocytes and fetal neural progenitors (16wf) as the normal controls.

first: Ping

last: Mao

first: Kaushal

last: Joshi

first: Jianfeng

last: Li

first: Sung-Hak

last: Kim

first: Peipei

first: Lucas

last: Santana-Santos

first: Soumya

last: Luthra

middle: R

first: Panayiotis

last: Benos

first: Luke

first: Maode

last: Wang

first: Bo

last: Hu

first: Shi-Yuan

last: Cheng

last: Sobol

first: Ichiro

last: Nakano


title: Non-canonical PRC1.1 targets active genes independent of H3K27me3 and is essential for leukemogenesis

status: Public on Nov 24 2015

first: Joost

last: Martens

summary: Polycomb proteins are classical regulators of stem cell self-renewal and cell lineage commitment and are frequently deregulated in cancer. Here we find that the non-canonical PRC1.1 complex, as identified by mass spectrometry-based proteomics, is critically important for human leukemic stem cells. Downmodulation of PRC1.1 complex members, like the DNA-binding subunit KDM2B, strongly reduces cell proliferation in vitro and delays or even abrogates leukemogenesis in vivo in humanized xenograft models. PRC1.1 components are significantly overexpressed in primary AML CD34+ cells. Besides a set of genes that is co-targeted by PRC1 and PRC2, ChIP-seq studies show that PRC1.1 also binds a distinct set of genes that are devoid of H3K27me3 suggesting a gene regulatory role independent of PRC2. This set encompasses genes involved in metabolism, which have transcriptionally active chromatin profiles. These data indicate that PRC1.1 controls distinct gene clusters involved in unique cell biological processes required for leukemic cell viability.

overall_design: K562 cells were transduced with lentiviral GFP-fusion vectors encoding GFP-CBX2, PCGF1-GPF, PCGF2-GFP, PCGF4-GFP, GFP-RING1A or GFP-RING1B. K562 cells expressing GFP-fusions at relatively low levels were sorted and expanded and subsequently crosslinked. ChIP reactions were performed using the following antibodies: anti-GFP (ab290, Abcam), anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (ab8580, Abcam), anti-H2AK119ub (D27C4, Cell Signaling Technology), and anti-KDM2B (ab137547, Abcam). Furthermore, ChIP reactions were performed using primary AML CD34+ and Peripheral Blood (PB) CD34+ cells using anti-H3K27me3 (07-449, Millipore), anti-H3K4me3 (ab8580, Abcam), anti-H2AK119ub (D27C4, Cell Signaling Technology), anti-KDM2B (ab137547, Abcam).

first: Vincent

last: van den Boom

first: Henny

last: Maat

first: Marjan

last: Rozenveld-Geugien

first: Ana

last: Sotoca

first: Jennifer

last: Jaques

first: Annet

last: Brouwers-Vos

first: Fabrizia

last: Fusetti

first: Hendrik

last: Stunnenberg

first: Edo

last: Vellenga

first: Anton

first: Aida

last: Rodríguez López

first: Richard

last: Groen

first: Huipin

last: Yuan

first: Jan

middle: J

last: Schuringa


title: Genome-wide candidate HAND2 target regions in mouse embryonic tissues

status: Public on Nov 11 2014

first: DBM Bioinformatics

last: Core Facility

summary: The bHLH transcriptional regulator HAND2 performs essential functions during development of the embryonic limb, heart and branchial arches, however, its genomic target regions remained largely unkown. Here, we uncover the range of candidate HAND2 target cis-regulatory modules in the major Hand2 expressing embryonic tissues during midgestation and focus on the transcriptional networks controlled by HAND2 in the developing limb. Our functional and genetic analysis reveals that in the early limb mesenchyme HAND2 directly regulates the expression of several transcription factors involved in the morphogenesis of limb proximal skeletal elements. In addition, HAND2 operates as a key factor in the establishment of anterior and posterior compartments, partly through direct binding to a Gli3 cis-regulatory module. Furthermore, HAND2 refines the posterior boundary of Gli3 expression domain through a relay mechanism mediated by Tbx3. These HAND2-dependent regulatory interactions are required to set the boundaries defining the localized expression of the Shh organizer region, which allows progression of distal limb outgrowth.

overall_design: Embryonic tissues including limb buds, hearts and branchial arches from 150 Hand23xFLAG or wild-type control embryos (NMRI strain) were pooled and processed for ChIP-Seq.

first: Marco

last: Osterwalder

first: Robert

last: Ivanek

first: Rolf

last: Zeller


title: Expression profile of Breast Cancer tumors in Brazilian women

status: Public on May 30 2014

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

institute: INCA

summary: On the basis of prognostic information provided by the PAM50 predictor, we evaluated how samples grouped relative to the other breast tumor subtypes. mRNA samples from 24 patients were amplified, labeled, and hybridized to the Affymetrix GeneChip Human Exon 1.0 ST array. After normalization and analysis of the microarray data using Partek® software (http://www.partek.com), we clustered all samples using the PAM50 predictor.

overall_design: We analyzed tumors from 24 patients with breast cancer using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by AffymetrixExpression Console and analysed using Partek software

first: Carolina

last: Panis

first: Eliana

last: Abdelhay


title: Effect of mifepristone on gene expression in Drosophila

status: Public on Jan 18 2015

city: Los Angeles

first: John

last: Tower

state: California

address: 1020 Childs Way, RRI213

department: Biological Sciences

institute: University of Southern California

summary: Illumina sequencing was used to assay the effect of mifepristone treatment on gene expression in adult Drosophila, including males, virgin females and mated females.

overall_design: Males of strain w[1118]; p53B[6] were crossed to virgins of w[1118]; rtTA(3)E2 and progeny males and virgins were collected over 48 hours.  One half of the virgins were mated to w[1118] males at ratio of 1:1 virgins to males for 4 days.  Mated females were then separated from the w[1118] males.  The mated females, males and virgins females were then maintained at approximately 20 flies per vial, on food with and without supplementation with 160ug/ml mifepristone for 12 days.  Total fly RNA was isolated from 20 animals per sample. Three replicate samples were generated for each type of flies: males, mated females and virgin females.

first: Matthew

middle: P

last: Salomon


title: A compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes

status: Public on Sep 09 2013

first: Joost

last: Martens

summary: Different mechanisms for CBF-MYH11 function in acute myeloid Leukemia (AML) with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of RUNX1 target genes. Here, through genome-wide CBF-MYH11 binding site analysis and quantitative interaction proteomics we found that CBF-MYH11 localizes to RUNX1 occupied promoters where it interacts with TAL1, FLI1 and TBP associated factors (TAFs) in the context of the hematopoietic transcription factors ERG, GATA2 and PU.1/SPI1 and the co regulators EP300 and HDAC1. Transcriptional analysis revealed that upon fusion protein knock down a subset of the CBF-MYH11 target genes show increased expression, confirming a role in transcriptional repression. However, the majority of CBF-MYH11 target genes, including genes implicated in hematopoietic stem cell (HSC) self-renewal such as ID1, LMO1 and JAG1, are actively transcribed and upon fusion protein knock down repressed. Together these results suggest an essential role for CBF-MYH11 in regulating expression of genes involved in maintaining a stem cell phenotype.

overall_design: 17 ChIP-seq samples using antibodies recognizing the indicated proteins and one RNA-seq file from ME-1 cells were analyzed. In addition 2 ChIP-seq profiles were generated using patient AML cells. A CBFβ-MYH11 inducible U937 system (U937CM) was used to examine binding patterns before (1 profile) and after (2 profiles) induction of CBFb-MYH11. In addition, expression was measured through RNA-seq analysis of the two states. The U937CM cells were maintained in the presence of tetracyclin (Tet, 1 uM) and grown in the absence of tetracycline for 3 days to induce expression of CBFβ-MYH11. Finally, a CBFb-MYH11 knock down system was developed in ME-1 cells. Two ME-1 cell lines were created, one with a stably integrated shRNA construct that targets CBFb-MYH11 (ME-1_knockdown) and one with a scrambled shRNA construct (ME-1_SCR). Expression of the shRNA constructs  was induced  using doxycyclin (dox; 1 mM) treatment for 3 days.

first: A

last: Mandoli

last: Singh

first: P

last: Jansen

first: B

last: Wierenga

first: H

last: Riahi

first: G

last: Franci

first: K

last: Prange

first: S

last: Saeed

first: E

first: M

last: Vermeulen

first: J


title: ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/Harvard

status: Public on Aug 30 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Philip Cayting mailto:pcayting@stanford.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding (Peaks).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et al. (2007) and Rozowsky et al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate <= 0.05 when comparing the number of peaks above threshold as compared the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.05 are considered to be significantly enriched compared to the input DNA control.

first: Michael

last: Snyder

first: Mark

last: Gerstein

first: Sherman

last: Weissman

first: Peggy

last: Farnham

first: Kevin

last: Struhl


title: Comparative expression analysis of the Arabidopsis strigolactone (SL)-response mutant, max2-3, and wild type (WT) plants (Col-0) under dehydration conditions.

status: Public on Nov 26 2013

city: Lubbock

first: chien

middle: Van

last: ha

address: 1006 Carton Avenue, Box 43135

institute: texas tech university

summary: To understand the role of SL-signaling components in water stress response, we have carried out comparative expression analysis of the SL-response max2-3 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and max2-3 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Chien

middle: V

last: Ha

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam-Son

last: Tran


title: Gene expression data of canine osteosarcoma primary tumors (Affymetrix Canine 2.0 array)

status: Public on Dec 18 2015

city: Fort Collins

first: Daniel

middle: L

last: Gustafson

state: CO

address: 300 West Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: The recently developed COXEN method (PMID: 17666531) has been used to successfully extrapolate gene signatures of drug sensitivity across different tumor histotypes.  We wanted to explore the utility of COXEN to predict chemosensitivity in canine cancer, specifically if we could extrapolate gene signatures identified in human datasets over to canine osteosarcoma tumors.  This dataset of canine osteosarcoma tumor samples has available clinical outcome data after patients had infected limbs amputated and were treated with doxorubicin and/or carboplatin.  We performed microarray analysis on this panel of tumor samples for validating our COXEN prediction models for doxorubicin or carboplatin sensitivity.

overall_design: Chemotherapy naive primary tumors were collected at the time of amputation and archived at the Flint Animal Cancer Center.  RNA was extracted from 33 frozen archived tumor samples, followed by microarray analysis.  The gene expression data was RMA preprocessed, scaled and were used as a independent test set to evaluate developed prediction models of sensitivity to doxorubicin or carboplatin.  Drug predictions were than compared to clinical outcome in these patients that received doxorubicin and/or carboplatin.

first: Jared

middle: S

last: Fowles


title: Epigenome analysis of normal and cancer, lung fibrosis and COPD fresh frozen tissue samples

status: Public on Nov 30 2015

city: Vienna

first: Matthias

last: Wielscher

address: Muthgasse 11

department: Health and Enviroment

institute: Austrian Institute of Technology

summary: In a comparative study the genome wide methylation levels using Illumina Infinium 450k chips were assigned. The specific methylation pattern of lung cancer patients (n=17), patients suffering from idiopathic lung fibrosis (n=37) as well as 32 patients suffering from chronic obstructive pulmonary disease and 43 DNA samples derived from healthy-lungs were determined. Lung biopsy samples were obtained by bronchoscopy. Thus obtained tissue was snap frozen in liquid nitrogen. Classification of lung fibrosis patients base on CT scans of the affected lung.

overall_design: Bisulfite converted DNA from the 129 samples were hybridised to the Illumina HumanMethylation450 BeadChip v1.2


title: Gene expression data of canine cancer cell lines and osteosarcoma primary tumors

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma [ChIP-Seq]

status: Public on Aug 04 2015

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: B-cell lymphomas frequently demonstrate inter-chromosomal translocations that lead to oncogene activation by heterologous distal regulatory elements.  We utilized a novel approach, termed ‘Pinpointing of Enhancer-Associated Rearrangements by Chromatin Immunoprecipitation’ or PEAR-ChIP, to simultaneously map enhancer activity and proximal rearrangements in lymphoma cell lines and patient biopsies. The method efficiently detects rearrangements within and adjacent to known cancer genes such as CCND1, BCL2, MYC, PDCD1LG2, NOTCH1, CIITA, and SGK1, as well as novel enhancer duplication events of likely oncogenic significance. We identify novel enhancer-like elements in the MYC locus that interact with the MYC promoter, are associated with germline polymorphisms that alter lymphoma risk, show lymphoma subtype-specific acetylation, and are silenced in lymphomas where MYC is activated by “enhancer hijacking” translocations. We also identify an array of BCL6-interacting enhancers that are subject to genomic alterations, are acetylated by the BCL6-activating transcription factor MEF2B, and target the MYC promoter in the context of a “pseudo-double-hit” t(3;8) genomic rearrangement linking the BCL6 and MYC loci. Our findings uncover diverse mechanisms by which genomic rearrangements can lead to aberrations in enhancer-mediated oncogene regulation.

overall_design: Examination of histone modifications and transcription factors in lymphoma cell lines and primary patient samples

first: Russell

last: Ryan

first: Bradley

last: Bernstein


title: Small RNA sequencing of transgenes silencing by paramutation in C. elegans

status: Public on Apr 01 2015

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

summary: In the nematode Caenorhabditis elegans, different small RNA-dependent gene silencing mechanisms act in the germline to initiate transgenerational gene silencing. Piwi-interacting RNAs (piRNAs) can initiate transposon and gene silencing by acting upstream of endogenous short interfering RNAs (siRNAs), which engage a nuclear RNA interference (RNAi) pathway to trigger transcriptional gene silencing. Once gene silencing has been established, it can be stably maintained over multiple generations without the requirement of the initial trigger and is also referred to as RNAe or paramutation. This heritable silencing depends on the integrity of the nuclear RNAi pathway. However, the exact mechanism by which silencing is maintained across generations is not understood.Here we demonstrate that silencing of piRNA targets involves the production of two distinct classes of small RNAs with different genetic requirements. The first class, secondary siRNAs, are localized close to the direct target site for piRNAs. Nuclear import of the secondary siRNAs by the Argonaute HRDE-1 leads to the production of a distinct class of small RNAs that map throughout the transcript, which we term tertiary siRNAs. Both classes of small RNAs are necessary for full repression of the target gene and can be maintained independently of the initial piRNA trigger. Consistently, we observed a form of paramutation associated with tertiary siRNAs. Once paramutated, a tertiary siRNA generating allele confers dominant silencing in the progeny regardless of its own transmission, suggesting germline-transmitted siRNAs are sufficient for multigenerational silencing.

overall_design: C. elegans strains containing transgenes silenced by piRNAs were crossed to strains with transgenes with similar sequences but without piRNA target sites, to investigate the spreading of silencing between transgenes mediated by small RNAs.  Mutant backgrounds were used to investigate the genetic requirements for this process.

first: Eric

last: Miska


title: Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition

status: Public on Mar 12 2014

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

institute: University of Basel